PCIF1

phosphorylated CTD interacting factor 1, the group of Protein phosphatase 1 regulatory subunits|7BS N6-adenosine DNA/RNA methyltransferases

Basic information

Region (hg38): 20:45934683-45948023

Previous symbols: [ "C20orf67" ]

Links

ENSG00000100982 ∙ NCBI:63935 ∙ OMIM:618626 ∙ HGNC:16200 ∙ Uniprot:Q9H4Z3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities	AR	Cardiovascular	Among other features, the condition can include cardiomyopathy, and awareness may allow early diagnosis and management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	28940097; 29808498; 30520571; 32985083

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCIF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCIF1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	0

Variants in PCIF1

This is a list of pathogenic ClinVar variants found in the PCIF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-45939007-A-G		not specified	Uncertain significance (Jan 23, 2024)
20-45939009-G-A		not specified	Uncertain significance (May 15, 2024)
20-45939023-C-G		not specified	Uncertain significance (Dec 20, 2021)
20-45939030-G-A		not specified	Uncertain significance (Jun 29, 2023)
20-45939037-C-T		not specified	Uncertain significance (Dec 04, 2024)
20-45939058-C-T		not specified	Uncertain significance (Jul 19, 2022)
20-45939099-A-G		not specified	Likely benign (Oct 29, 2024)
20-45939111-C-G		not specified	Uncertain significance (Jun 21, 2023)
20-45939316-G-A		not specified	Uncertain significance (Dec 27, 2023)
20-45940532-A-C		not specified	Uncertain significance (Oct 26, 2021)
20-45940536-C-A		not specified	Uncertain significance (Aug 27, 2024)
20-45940875-A-C		not specified	Uncertain significance (Oct 13, 2023)
20-45940897-C-A		not specified	Uncertain significance (Jun 16, 2024)
20-45940926-C-A		not specified	Uncertain significance (Mar 15, 2023)
20-45941094-A-G		not specified	Uncertain significance (Sep 08, 2023)
20-45941132-G-A		not specified	Uncertain significance (Oct 08, 2024)
20-45941150-T-G		not specified	Uncertain significance (Oct 06, 2021)
20-45941159-A-G		not specified	Uncertain significance (Dec 14, 2023)
20-45941178-A-G		not specified	Uncertain significance (Nov 16, 2021)
20-45941183-C-T		not specified	Uncertain significance (Jan 23, 2024)
20-45943676-C-T		not specified	Uncertain significance (Aug 16, 2021)
20-45943739-C-T		not specified	Uncertain significance (Apr 28, 2023)
20-45944907-G-A		not specified	Uncertain significance (Aug 17, 2022)
20-45944911-C-T		not specified	Uncertain significance (Nov 21, 2023)
20-45945767-C-G		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCIF1	protein_coding	protein_coding	ENST00000372409	15	13396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000123	125733	0	5	125738	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.41	315	461	0.684	0.0000308	4570
Missense in Polyphen		65	165.22	0.39341		1584
Synonymous	-0.316	188	183	1.03	0.0000120	1400
Loss of Function	5.61	2	40.6	0.0493	0.00000235	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000588	0.0000588
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in transcription elongation or in coupling transcription to pre-mRNA processing through its association with the phosphorylated C-terminal domain (CTD) of RNAPII largest subunit.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.00592
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.116
• hipred: Y
• hipred_score: 0.673
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcif1

Gene ontology

• Biological process: negative regulation of phosphatase activity
• Cellular component: nucleus;nucleoplasm;microtubule cytoskeleton;intercellular bridge